7XPD

Cryo-EM structure of the T=3 lake sinai virus 2 virus-like capsid at pH 6.5

Summary for 7XPD

• Entry DOI: 10.2210/pdb7xpd/pdb
• EMDB information: 33370
• Descriptor: Capsid protein alpha (1 entity in total)
• Functional Keywords: virus like particle
• Biological source: Lake Sinai virus 2
• Total number of polymer chains: 3
• Total formula weight: 172032.93

Authors

Chen, N.C.,Wang, C.H.,Chen, C.J.,Yoshimura, M.,Guan, H.H.,Chuankhayan, P.,Lin, C.C. (deposition date: 2022-05-04, release date: 2023-02-08, Last modification date: 2024-05-08)

Primary citation

Chen, N.C.,Wang, C.H.,Yoshimura, M.,Yeh, Y.Q.,Guan, H.H.,Chuankhayan, P.,Lin, C.C.,Lin, P.J.,Huang, Y.C.,Wakatsuki, S.,Ho, M.C.,Chen, C.J.
Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions.
Nat Commun, 14:545-545, 2023

PubMed Abstract: Understanding the structural diversity of honeybee-infecting viruses is critical to maintain pollinator health and manage the spread of diseases in ecology and agriculture. We determine cryo-EM structures of T = 4 and T = 3 capsids of virus-like particles (VLPs) of Lake Sinai virus (LSV) 2 and delta-N48 LSV1, belonging to tetraviruses, at resolutions of 2.3-2.6 Å in various pH environments. Structural analysis shows that the LSV2 capsid protein (CP) structural features, particularly the protruding domain and C-arm, differ from those of other tetraviruses. The anchor loop on the central β-barrel domain interacts with the neighboring subunit to stabilize homo-trimeric capsomeres during assembly. Delta-N48 LSV1 CP interacts with ssRNA via the rigid helix α1', α1'-α1 loop, β-barrel domain, and C-arm. Cryo-EM reconstructions, combined with X-ray crystallographic and small-angle scattering analyses, indicate that pH affects capsid conformations by regulating reversible dynamic particle motions and sizes of LSV2 VLPs. C-arms exist in all LSV2 and delta-N48 LSV1 VLPs across varied pH conditions, indicating that autoproteolysis cleavage is not required for LSV maturation. The observed linear domino-scaffold structures of various lengths, made up of trapezoid-shape capsomeres, provide a basis for icosahedral T = 4 and T = 3 architecture assemblies. These findings advance understanding of honeybee-infecting viruses that can cause Colony Collapse Disorder.

PubMed: 36726015
DOI: 10.1038/s41467-023-36235-3

Experimental method

ELECTRON MICROSCOPY (3.74 Å)